7KI9

Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001912

• PDB DOI: https://doi.org/10.2210/pdb7KI9/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Mycobacterium ulcerans Agy99
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-10-23 Released: 2021-07-07 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.165 
• R-Value Work: 0.134 
• R-Value Observed: 0.136 

Starting Model: experimental

Literature

Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001912

Abendroth, J.A., Dranow, D.M., Zigweid, R.M., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 20.21 kDa 
• Atom Count: 1,615 
• Modelled Residue Count: 166 
• Deposited Residue Count: 173 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	173	Mycobacterium ulcerans Agy99	Mutation(s): 2  Gene Names: dfrA, MUL_2179 EC: 1.5.1.3
UniProt
Find proteins for A0PQG8 (Mycobacterium ulcerans (strain Agy99)) Explore A0PQG8  Go to UniProtKB:  A0PQG8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
WFJ (Subject of Investigation/LOI)	C [auth A]	1-[2-(3-{[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]methyl}azetidin-1-yl)phenyl]piperidine-4-carboxylic acid C22 H30 N6 O3 HUNFOZYRLCOIAK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.165 
• R-Value Work: 0.134 
• R-Value Observed: 0.136 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/m37ki9

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.43	α = 90
b = 70.79	β = 111.48
c = 36.18	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-07 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2021-07-07
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description